A central question in eukaryotic chromosome biology is how the normal ends of linear chromosomes, telomeres, are distinguished from double strand breaks. One well-established mechanism is the recognition of telomeric-specific sequences by sequence specific DNA binding proteins such as human TRF2. However, several observations demonstrate that other mechanisms play an essential, but poorly understood role in telomere protection. Among the most striking examples are studies in Drosophila in which it is possible to isolate and maintain chromosomes with no telomere-specific sequences at their ends. These studies indicate that a sequence-independent, i.e. epigenetic, mechanism regulates telomere protection in Drosophila. Two cellular pathways have been implicated in Drosophila telomere protection. The chromatin-associated protein HP1 and a telomere-specific binding partner, HOAP, are localized to telomeres and are required for their protection. We have also found that mutations in the DNA damage response kinases ATM and ATR lead to loss of telomeric HP1-HOAP and loss of telomere protection. Recognition of chromosome ends by ATM/ATR kinases could provide a sequence-independent means to recruit proteins to telomeres, but this model does not address how these proteins distinguish between chromosome breaks and telomeres. We hypothesize that DNA damage response pathways act by a homeostatic mechanism to protect telomeres by recruiting HP1-HOAP complexes to incompletely protected telomeres. To test this model, we will probe the activity of ATM/ATR kinases at normal telomeres and at telomeres with defective HP1 spreading. In addition, our preliminary results suggest that the mutator-2 gene may act as a link between the DNA damage response pathway and HP1, but that it also has a second function fusing telomeres when they become completely unprotected. By understanding the role of mutator-2 at telomeres, we may learn how the damage response is modulated at telomeres and at chromosome breaks. Telomeres appear to play a central role in human cancer and aging. These studies will help elucidate a new category of epigenetic inheritance, sequence-independent regulation of telomere function. Given that both HP1 and DNA damage response pathways play roles at human telomeres, understanding telomere function in Drosophila may lead to new ways to shorten or extend telomeres in humans. PUBLIC HEALTH RELEVANCE: Telomeres, the normal ends of chromosomes, appear to play important roles in human aging and cancer. We are using the model organism Drosophila melanogaster to study how proteins that recognize damaged chromosomes also help regulate telomere function. Improved understanding of telomere regulation may provide new strategies to modulate human aging and cancer.